With a pullover type machine the upper body is held more stable. With a BB/DB more supporting muscles are brought into play. The point of resistence is on the elbows (I hope), which gives a pullover machine a better advantage, with less stress on the muscle link starting from the grip to the shoulder area. The main focus being on the lat's themselves. The center of gravity is also changed (sitting vs, lying) giving a different muscle strength curve (and stress) to the exercise. Nautilis machines would be my first choice because of the cam gear and the front curl grip lat bar for pre-exhaustion style training. I have used both the Nautilis & free weights, with both having a place in most trainee's workout plan.
If one finds pain or discomfort in the BB/DB pullover (or any other exercisae for that matter) than don't do that exercise. Like the squat, some people can not preform the exercise without discomfort. No matter how many people tell you that you must do squats, be your own judge. If their not for you, than their not for you.
I find that a lot people are way too stiff in the shoulder girdle area when first trying to do a pullover (or PBN's). Mistake being that they try to rush the weight their using, too soon, before ready for heavier stuff. There may even be a lurking shoulder problem one is not aware of that comes to light from doing pullovers or any other exercise. It seems to me that a lot of trainee's who spend too much of their workouts on machines tend to be not that flexable in certain body muscle/joint groups. May be wrong but that's the impression I get. The pullover should be appraoched with caution at first until getting use to it. If you can do pullovers without any problems than you might try the following. A set of straight arm pullovers followed immediately by heavier bent arm pullovers. A very fine upper body mass builder. Good Luck.
